314 lines
12 KiB
Mathematica
314 lines
12 KiB
Mathematica
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function [sel,sell,selb] = select(tr,varargin)
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%SELECT Selects tree branches and leaves.
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%
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% S = SELECT(T,N) returns a logical vector S of size [NUMNODES x 1]
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% indicating N closest nodes to the root node of the phylogenetic tree
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% object T (NUMNODES = NUMLEAVES + NUMBRANCHES). The first criteria used
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% is branch levels, then patristic distance, also known as tree distance.
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% By default SELECT, uses INF as the value of N, therefore SELECT(T) will
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% return a vector of 'trues'.
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%
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% S = SELECT(...,'REFERENCE',R) changes the reference point(s) to measure
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% the closeness. R can be 'root' (default) or 'leaves'. When using
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% 'leaves', a node to be tested may have different distances to its
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% descendant leaves, which are the references (e.g. a non-ultrametric
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% tree), if this the case the minimum distance to any descendant leaf
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% will be considered. R may also be an index which points to any node of
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% the tree.
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%
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% S = SELECT(...,'CRITERIA',C) changes the criteria used to measure
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% closeness. If C='levels' (default) then the first criteria is branch
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% levels and then patristic distance. If C='distance' then the first
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% criteria is patristic distance and then branch levels.
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%
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% S = SELECT(...,'THRESHOLD',V) selects all the nodes which closeness is
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% less or equal than the threshold value V. Observe that either
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% 'criteria' or either 'reference' can be used. If N is not specified
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% N = INF, otherwise the output can be further size limited by N.
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%
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% S = SELECT(...,'EXCLUDE',E) sets a post-filter which excludes all the
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% branch nodes from S when E=='branches' or all the leaf nodes when
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% E=='leaves'. The default is 'none'.
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%
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% S = SELECT(...,'PROPAGATE',P) activates a post-functionality which
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% propagates the selected nodes to the leaves when P=='toleaves' or
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% towards the root finding a common ancestor when P=='toroot'. The
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% default is 'none', P may also be 'both'. 'PROPAGATE' switch acts after
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% 'EXCLUDE' switch.
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%
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% [S,SELLEAVES,SELBRANCHES] = SELECT(...) returns two additional logical
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% vectors, one for the selected leaves and one for the selected branches.
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%
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% Examples:
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%
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% % Load a phylogenetic tree created from a protein family:
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% tr = phytreeread('pf00002.tree');
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%
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% % To find close products for a given protein (e.g. vips_human):
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% ind = getbyname(tr,'vips_human');
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% [sel,sel_leaves] = select(tr,'criteria','distance',...
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% 'threshold',0.6,'reference',ind);
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% view(tr,sel_leaves)
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%
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% % To find potential outliers in the tree use:
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% [sel,sel_leaves] = select(tr,'criteria','distance','threshold',.3,...
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% 'reference','leaves','exclude','leaves','propagate','toleaves');
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% view(tr,~sel_leaves)
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%
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%
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% See also PHYTREE, PHYTREE/GET, PHYTREE/PDIST, PHYTREE/PRUNE, PHYTREETOOL.
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%
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% Copyright 2003-2006 The MathWorks, Inc.
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% $Revision: 1.1.6.7.2.1 $ $Author: batserve $ $Date: 2006/07/27 21:37:50 $
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if numel(tr)~=1
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error('Bioinfo:phytree:select:NoMultielementArrays',...
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'Phylogenetic tree must be an 1-by-1 object.');
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end
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% set defaults
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V=inf;
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CriteriaIsDistance = false;
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ReferenceIs = 'root';
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ExcludeSwitch = false;
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PostPropagate = false;
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% check is first argument is N, otherwise set N to default
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if (nargin>1 && isnumeric(varargin{1}) && isreal(varargin{1}))
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N = floor(varargin{1});
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first_arg = 3;
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else
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N = inf;
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first_arg = 2;
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end
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numBranches = size(tr.tree,1);
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numLeaves = numBranches + 1;
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numLabels = numBranches + numLeaves;
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% identify input arguments
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if nargin - first_arg + 1 > 0
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if rem(nargin - first_arg,2) == 0
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error('Bioinfo:phytree:select:IncorrectNumberOfArguments',...
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'Incorrect number of arguments to %s.',mfilename);
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end
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okargs = {'reference','criteria','threshold','exclude','propagate'};
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for j=first_arg - 1 : 2 : nargin - first_arg + 1
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pname = varargin{j};
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pval = varargin{j+1};
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k = find(strncmpi(pname,okargs,numel(pname)));
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if isempty(k)
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error('Bioinfo:phytree:select:UnknownParameterName',...
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'Unknown parameter name: %s.',pname);
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elseif length(k)>1
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error('Bioinfo:phytree:select:AmbiguousParameterName',...
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'Ambiguous parameter name: %s.',pname);
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else
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switch(k)
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case 1 % reference
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if islogical(pval)
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if numel(pval)==numLabels
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pval = pval(:)==true;
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elseif numel(pval)==numLeaves
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pval = [pval(:);false(numBranches,1)];
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elseif numel(pval)==numBranches
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pval = [false(numLeaves,1);pval(:)];
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else
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error('Bioinfo:phytree:select:InvalidSizeLogicalReferenceNode',...
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'When reference node is a logical vector it must contain NUMNODES, NUMLEAVES or NUMBRANCHES elements.')
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end
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pval = find(pval);
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ReferenceIs = 'node';
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if numel(pval) ~= 1
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error('Bioinfo:phytree:select:InvalidValuesLogicalReferenceNode',...
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'When reference node is a logical vector one element must be true and all others false.')
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else
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ReferenceNode = pval;
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end
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elseif isnumeric(pval)
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ReferenceIs = 'node';
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if numel(pval) ~= 1
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error('Bioinfo:phytree:select:InvalidSizeReferenceNode',...
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'Reference node must be scalar.')
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elseif all(pval~=1:numLabels)
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error('Bioinfo:phytree:select:InvalidValueReferenceNode',...
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'Incorrect reference node.')
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else
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ReferenceNode = pval;
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end
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else
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h = strmatch(lower(pval),{'root','leaves'}); %#ok
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if numel(h)
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switch(h)
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case 1
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ReferenceIs = 'root';
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case 2
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ReferenceIs = 'leaves';
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end
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else error('Bioinfo:phytree:select:InvalidStringReferenceNode',...
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'Invalid string for the reference node.');
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end
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end
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case 2 % criteria
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h = strmatch(lower(pval),{'distance','levels'}); %#ok
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if numel(h)
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CriteriaIsDistance = (h == 1);
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else error('Bioinfo:phytree:select:InvalidCriteria',...
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'Invalid string for criteria.');
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end
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case 3 % threshold
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V = pval;
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if (~isnumeric(V) || ~isreal(V) || numel(V)>1)
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error('Bioinfo:phytree:select:InvalidThreshold',...
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'Invalid value for V.');
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end
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case 4 % exclude
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h = strmatch(lower(pval),{'branches','leaves','none'}); %#ok
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if numel(h)
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switch(h)
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case 1
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ExcludeSwitch = true;
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ExcludeType = 'branches';
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case 2
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ExcludeSwitch = true;
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ExcludeType = 'leaves';
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case 3
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ExcludeSwitch = false;
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end
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else error('Bioinfo:phytree:select:InvalidExcludeOption',...
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'Invalid string for exclude switch.');
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end
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case 5 % propagate
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h = strmatch(lower(pval),{'toleaves','toroot','both','none'}); %#ok
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if numel(h)
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switch(h)
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case 1
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PostPropagate = true;
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PostPropagateType = 'toleaves';
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case 2
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PostPropagate = true;
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PostPropagateType = 'toroot';
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case 3
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PostPropagate = true;
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PostPropagateType = 'both';
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case 4
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PostPropagate = false;
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end
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else error('Bioinfo:phytree:select:InvalidPostPropagate',...
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'Invalid string for post-propagate switch.');
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end
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end % switch(k)
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end % if ...
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end % for j=...
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end % nargin
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% calculate the distance (and levels) of every node to the reference
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levels2Ref = zeros(numLabels,1);
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switch ReferenceIs
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case 'root'
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% calculate the distance to the root for every node
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dist2Ref = tr.dist;
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for ind = numBranches:-1:1
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dist2Ref(tr.tree(ind,:)) = ...
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dist2Ref(tr.tree(ind,:)) + dist2Ref(ind+numLeaves);
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levels2Ref(tr.tree(ind,:)) = levels2Ref(ind+numLeaves) + 1;
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end
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case 'leaves'
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% calculate the distance to the closest leaf for every node
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dist2Ref = zeros(numLabels,1);
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for ind = 1:numBranches
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dist2Ref(ind+numLeaves) = ...
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min(dist2Ref(tr.tree(ind,:))+tr.dist(tr.tree(ind,:)));
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levels2Ref(ind+numLeaves) = min(levels2Ref(tr.tree(ind,:))) + 1;
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end
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case 'node'
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refVector = zeros(numLabels,1);
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refVector(ReferenceNode)=1;
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dist2Ref = pdist(tr,'SquareForm',true,'nodes','all')...
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* refVector;
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tr.dist = ones(numLabels,1); % to count now levels !
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levels2Ref = pdist(tr,'SquareForm',true,'nodes','all') ...
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* refVector;
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end
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% applies the threshold value
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if CriteriaIsDistance
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sel = dist2Ref < V;
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else % ~CriteriaIsDistance
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sel = levels2Ref < V;
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end % if CriteriaIsDistance
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% needs to remove additional nodes because of N
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if sum(sel)>N
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if CriteriaIsDistance
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[dum,h]=sortrows([dist2Ref levels2Ref]); %#ok
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else % ~CriteriaIsDistance
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[dum,h]=sortrows([levels2Ref dist2Ref]); %#ok
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end % if CriteriaIsDistance
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g=h(sel(h));
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sel(g(N+1:end))=false;
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end
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% exclude option
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if ExcludeSwitch
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switch ExcludeType
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case 'branches'
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sel((1+numLeaves):numLabels) = false;
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case 'leaves'
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sel(1:numLeaves) = false;
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end
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end
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% post-propagate option
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if PostPropagate
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% expands all the current nodes towards the leaves
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if any(strcmp({'toleaves','both'},PostPropagateType))
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for ind = numBranches:-1:1
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if sel(ind+numLeaves)
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sel(tr.tree(ind,:))=true;
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end
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end
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end
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% propagates towards the root finding the common ancestors
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if any(strcmp({'toroot','both'},PostPropagateType))
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% find closest common branch for every pair of nodes
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% diagonal is invalid ! but not needed
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% initializing full matrix
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commf = zeros(numLabels,'int16');
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children = false(1,numLabels);
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for ind = numBranches:-1:1
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children(:) = false;
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children(ind+numLeaves) = true;
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for ind2 = ind:-1:1
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if children(ind2+numLeaves)
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children(tr.tree(ind2,:))=true;
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end
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end
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commf(children,children)=int16(ind);
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end
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commf = commf(sel,sel);
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commf = commf - diag(diag(commf));
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commf = unique(commf(commf(:)>0));
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sel(commf+numLeaves) = true;
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% now propagates towards the common ancestor
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for ind = 1:double(max(commf))
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if any(sel(tr.tree(ind,:)))
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sel(ind+numLeaves) = true;
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end
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end
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end
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end
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if nargout > 1
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sell = sel(1:numLeaves);
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end
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if nargout > 2
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selb = sel(numLeaves+1:numLabels);
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end
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